Best protein S epitope is bound to its respective Major Histocompatibility Complex Class I alleles according to molecular dynamics results
| Allele | PDB | Peptide | Code | %Rank | OPPA prediction | Average RMSD (Å) |
| HLA-A*01:01 | 4NQX | NLDSKVGGNY | pep2 | 0.1041 | 0.7882 | 2.5624 |
| HLA-A*01:01 | 4NQX | GWTAGAAAYY | pep3 | 0.2305 | 0.5358 | 2.6896 |
| HLA-A*02:01 | 4L29 | KLNDLCFTNV | pep6 | 0.2287 | 2.6927 | 1.1479 |
| HLA-A*02:01 | 4L29 | FELLHAPATV | pep7 | 0.3513 | 0.5982 | 1.1796 |
| HLA-A*11:01 | 1X7Q | VTLADAGFIK | pep15 | 0.1366 | 0.8702 | 2.1979 |
| HLA-A*11:01 | 1X7Q | SLIDLQELGK | pep18 | 0.2777 | 1.0275 | 1.9232 |
| HLA-A*24:02 | 2BCK | TYVPAQEKNF | pep24 | 0.0424 | 0.7276 | 2.0925 |
| HLA-A*68:01 | 6PBH | HVTYVPAQEK | pep65 | 0.2517 | 1.0786 | 1.1007 |
| HLA-A*23:01 | swissmodel | CYFPLQSYGF | pep83 | 0.3803 | 0.7776 | 2.8308 |
| HLA-A*26:01 | swissmodel | EILDITPCSF | pep85 | 0.1991 | 1.2698 | 1.7413 |
| HLA-A*26:01 | swissmodel | GWTAGAAAYY | pep87 | 0.2372 | 0.5358 | 1.9260 |
| HLA-A*30:02 | swissmodel | IGAEHVNNSY | pep92 | 0.4353 | 1.2671 | 1.5989 |
| HLA-A*31:01 | swissmodel | RKSNLKPFER | pep96 | 0.4348 | 0.8187 | 2.4331 |
| HLA-B*07:02 | 5EO0 | TPCSFGGVSV | pep59 | 0.3909 | 1.7080 | 2.7139 |
| HLA-B*51:01 | 5VUE | VAYSNNSIAI | pep70 | 0.4565 | 1.0545 | 1.2241 |
| HLA-B*35:01 | 1XH3 | LPIGINITRF | pep72 | 0.0959 | 1.3027 | 2.2773 |
| HLA-B*35:01 | 1XH3 | QIPFAMQMAY | pep73 | 0.2719 | 1.2149 | 1.6030 |
| HLA-B*35:01 | 1XH3 | FPNITNLCPF | pep75 | 0.4307 | 1.3964 | 2.4222 |
| HLA-B*44:02 | 1M6O | TESNKKFLPF | pep79 | 0.4851 | 1.0405 | 1.4687 |
| HLA-B*35:03 | swissmodel | LPIGINITRF | pep97 | 0.1519 | 1.3027 | 2.0459 |
| HLA-B*35:03 | swissmodel | LPFFSNVTWF | pep98 | 0.4127 | 0.6567 | 0.4809 |
| HLA-C*05:01 | swissmodel | LVDLPIGINI | pep103 | 0.1770 | 1.3499 | 0.2044 |
| HLA-C*07:01 | swissmodel | IVRFPNITNL | pep105 | 0.1311 | 0.5548 | 4.0092 |
| HLA-C*15:02 | swissmodel | AVRDPQTLEI | pep109 | 0.4849 | 0.7083 | 2.5140 |
It is possible to see the Protein Data Bank (PDB) ID for the structures used (or the indication that the structure was modelled using Swiss-model); the amino acid sequence; the code that we used during the simulations; %Rank value from NetMHC Pan; Vaxijen’s OPPA score and average root mean squared deviation (RMSD) for the docking simulations according to CABS dock.
HLA, Human Leukocyte Antigen.